[gmx-users] Re grompp and mdrun output files

Giuseppina La Sala giuseppina.lasala2 at unibo.it
Fri Jul 25 09:30:46 CEST 2014

Hi Melsa,
I think that your problem could belong to the fact that in the .xtc file you do not write all the frames, but every n-steps. Thus, the last frame of your xtc file is a multiple of n-step (a discrete value) and not necessary the real last one, that for sure is represented by md300.gro.


Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] per conto di Melsa Rose Ducut [ducut_melsarose at yahoo.com]
Inviato: venerdì 25 luglio 2014 6.50
A: gromacs.org_gmx-users at maillist.sys.kth.se
Oggetto: [gmx-users] Re grompp and mdrun output files

Hi GROMACS users,

I typed the command
grompp -f md300.mdp -c equi_new.gro -n dex.ndx -p topol.top -maxwarn 1 -o md300.tpr

then this command

mdrun -v -deffnm md300

So, I was expecting that the md300.gro output file will be same to the last frame when I load the md300.xtc on the equi_new.gro file on vmd. However, that is not the case. Can anyone please enlighten me about this? Thanks.

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